A Unified Approach to Reverse Engineering and Data Selection for Unique Network Identification

SIAM Journal on Applied Dynamical Systems, Volume 23, Issue 1, Page 592-615, March 2024.
Abstract.Due to cost concerns, it is optimal to gain insight into the connectivity of biological and other networks using as few experiments as possible. Data selection for unique network connectivity identification has been an open problem since the introduction of algebraic methods for reverse engineering for almost two decades. In this manuscript we determine what data sets uniquely identify the unsigned wiring diagram corresponding to a system that is discrete in time and space. Furthermore, we answer the question of uniqueness for signed wiring diagrams for Boolean networks. Computationally, unsigned and signed wiring diagrams have been studied separately, and in this manuscript we also show that there exists an ideal capable of encoding both unsigned and signed information. This provides a unified approach to studying reverse engineering that also gives significant computational benefits.